I thought they looked like chains because the "windows" blend in with the background water, making it seem like loops in a chain.
You should also consider grounding them more by giving them actual ground (ie, let us see the bottom. Subsequently, the top of some of the farther spires are hard to see) to establish them as buildings.
Alternatively, you can add more detail to make them stand out, but considering the art direction as a whole, I think the former might be the best decision so it won't compromise the rest of your work 